I cannot figure out how to use odfWeave to produce tables eith
right-aligned columns. None of the examples show this and I'm completely
confused on how to achieve this. Could someone share a simple example?
Rick B.
__
R-help@stat.math.ethz.ch mailing
I cannot figure out how to use odfWeave to produce tables with
right-aligned columns. None of the examples show this and I'm completely
confused on how to achieve this. Could someone share a simple example?
Rick B.
__
R-help@stat.math.ethz.ch mailing
If you create plots and use odfWeave to create an odf text document, the
default for figures is png bitmap graphics. The only way I've found to
insert eps graphics is to first create the eps graphic using the
postscript driver and then use odfInsertPlot. I've tried to use
getImageDefs and
The publisher requires embedded fonts and the eps files that R produces
don't pass its tests. How can I force the fonts (just default fonts) to
be embedded. embedFonts seems to only embed unusual fonts, not the
default ones that are used in a simple eps generated by using
postscript.
I've tried:
On Mon, 2007-02-19 at 15:11 -0600, Ranjan Maitra wrote:
The error is different now. It now cannot find Xext library. Do a yum search
on this and install that.
yum provides libXext
which will give you the package Xext which needs to be installed.
You may also need to install the
Summarizing:
I'm running R 2.4.1 on a current FC6 32-bit system. In order to have the
rgl R package install, I needed to install both mesa-libGLU-devel (FC6
version is 6.5.1-9) and libXext-devel (FC6) rpm packages. Thanks to
everyone who commented.
Rick B.
I'm running R 2.4.1 (with the latest versions of all packages) on an
FC6 32-bit system. When I try to install the rgl package, compilation
fails:
install.packages(rgl)
--- Please select a CRAN mirror for use in this session ---
Loading Tcl/Tk interface ... done
trying URL
On Mon, 2007-02-19 at 19:56 +, Oleg Sklyar wrote:
Check again your error message:
opengl.hpp:24:20: error: GL/glu.h: No such file or directory
you need to install
mesa-libGLU-devel FC6 version is 6.5.1-7
which will provide development files for glut3. Needless to say the
above
I need to generate autocorrelated binary data. I've found references to
the IEKS package but none of the web pages currently exist. Does anyone
know where I can find this package or suggest another package?
Rick B.
__
R-help@stat.math.ethz.ch mailing
I'm estimating models using lme in a for loop. Sometimes the model
doesn't converge or there are other problems. This causes the evaluation
to stop prematurely. I can't remember the function name that I need to
use to allow the loop to continue until the end. Could someone remind me
the name of
I'm running simulation using lme and sometimes the estimated
variance-covariance matrix is not positive definite so that the
intervals function won't work for the random effect coefficients. I've
tried varcomp from the ape package but this does not return all the
coefficients. How can I extract
I'm using groupedData from nlme. I set up a groupedData data.frame with
outer=~group1. When I try to plot with outer=TRUE, I get subscript out
of bounds. This happens most of the time. When it works, I get
spaghetti-type plots for comparing groups. But I don't understand why it
doesn't usually
Using the weight argument with a variance function in lme (nlme), you
can allow for heteroscedasticity of the within-group error. Is there a
way to do this for the other variance components? For example, suppose
you had subjects, days nested within subjects, and visits nested within
days within
On Sun, 2006-10-29 at 11:06 -0800, Spencer Graves wrote:
I can think of two ways to get confidence intervals on intraclass
correlations (ICCs) and more accurate intervals for variance
components: (1) modifying 'simulate.lme' to store the estimated
variance components as well as
I'm using the lme function in nmle to estimate the variance components
of a fully nested two-level model:
Y_ijk = mu + a_i + b_j(i) + e_k(j(i))
lme computes estimates of the variances for a, b, and e, call them v_a,
v_b, and v_e, and I can use the intervals function to get confidence
intervals.
event.nab.2 is 0/1 and I dichotomized va to get va.2 to see if I could
get geeglm to work. glm has no problem with the data but geeglm chokes.
Each subject (patient.id) has at most 2 observations and more than 3/4
of the subjects have 2 observations. I have even worse problems trying
to use
Is there a way (simple or not) to get the marginal prediction from lme
(in nlme) and/or lmer (in lme4)?
Rick B.
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R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
On Wed, 2006-08-23 at 06:43 +1000, Andrew Robinson wrote:
Rick,
if by marginal prediction, you mean the prediction without random
effects, then use the level argument. See ?predict.lme or ?fitted.lme
If not then I don't know :)
Cheers
Andrew
Thanks. I'm familiar with level in
I can't find a way to retrieve z values and p-values from the output
from lmer in the lme4 package. How is this done?
Rick B.
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
On Mon, 2006-08-21 at 16:52 -0400, Rick Bilonick wrote:
I can't find a way to retrieve z values and p-values from the output
from lmer in the lme4 package. How is this done?
Rick B.
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch
On Wed, 2006-08-16 at 17:01 -0400, John Fox wrote:
Dear Rick,
It's unclear to me what you mean by constraining each column of the factor
matrix to sum to one. If you intend to constrain the loadings on each
factor to sum to one, sem() won't do that, since it supports only equality
sem() handles only equality constraints among parameters, and this model
requires linear inequality constraints.
I'm aware of SEM software that handles inequality constraints, but I'm not
aware of anything in R that will do it out of the box. One possibility is
to write out the likelihood
On Wed, 2006-08-16 at 08:47 -0400, John Fox wrote:
Dear Rick,
There are a couple of problems here:
(1) You've fixed the error variance parameters for each of the observed
variables to 1 rather than defining each as a free parameter to estimate.
For example, use
X1 - X1, theta1, NA
I'm using specify.model for the sem package. I can't figure out how to
represent the residual errors for the observed variables for a CFA
model. (Once I get this working I need to add some further constraints.)
Here is what I've tried:
model.sa - specify.model()
F1 - X1,l11, NA
F1 -
I'm fitting a mixed effects model:
fit.1 - lme(y~x,random=~1|id,data=df)
There are two different observations for each id for both x and y. When
I use plot(fit.1), there is a strong increasing linear trend in the
residuals versus the fitted values (with no outliers). This also happens
if I use
On Wed, 2006-08-09 at 15:04 -0500, Douglas Bates wrote:
On 8/9/06, Rick Bilonick [EMAIL PROTECTED] wrote:
I'm fitting a mixed effects model:
fit.1 - lme(y~x,random=~1|id,data=df)
There are two different observations for each id for both x and y. When
I use plot(fit.1
On Wed, 2006-08-09 at 15:04 -0500, Douglas Bates wrote:
On 8/9/06, Rick Bilonick [EMAIL PROTECTED] wrote:
I'm fitting a mixed effects model:
fit.1 - lme(y~x,random=~1|id,data=df)
There are two different observations for each id for both x and y. When
I use plot(fit.1
I use R to create .eps graphics and then use oodraw to convert them
to .emf versions. (One reason I do this is that OOo tends to
re-size .eps files and I haven't found a way to stop it or change it
once the graph is resized. .emf files are not distorted by OOo -
fortunately.) I use a command like:
Please ignore this - it was sent to the wrong list by mistake.
Rick B.
On Mon, 2006-08-07 at 23:23 -0400, Rick Bilonick wrote:
I use R to create .eps graphics and then use oodraw to convert them
to .emf versions. (One reason I do this is that OOo tends to
re-size .eps files and I haven't
On Fri, 2006-08-04 at 19:37 -0400, Jim Lemon wrote:
Hi all,
I have finally gotten the prettyR package going (many thanks to Kurt
Hornik for his patience).
prettyR is a set of functions that allows the user to produce HTML
output from R scripts. Given an R script that runs properly, an
I'm estimating two models for data with n = 179 with four clusters (21,
70, 36, and 52) named siteid. I'm estimating a logistic regression model
with random intercept and another version with random intercept and
random slope for one of the independent variables.
fit.1 -
On Wed, 2006-06-28 at 11:04 -0400, harry wills wrote:
Thanks for the help Dimitris,
However I still have a question, this time I'll be more specific,
the following is my SAS code
proc mixed data=Reg;
class ID;
model y=Time Time*x1 Time*x2 Time*x3 /S;
random
On Fri, 2006-06-23 at 21:38 -0700, Spencer Graves wrote:
Permit me to try to repeat what I said earlier a little more clearly:
When the outcomes are constant for each subject, either all 0's or all
1's, the maximum likelihood estimate of the between-subject variance in
Inf. Any
On Tue, 2006-06-20 at 20:27 +0200, Göran Broström wrote:
On 6/19/06, Rick Bilonick [EMAIL PROTECTED] wrote:
On Sun, 2006-06-18 at 13:58 +0200, Douglas Bates wrote:
If I understand correctly Rick it trying to fit a model with random
effects on a binary response when there are either 1 or 2
On Wed, 2006-06-21 at 08:35 -0700, Spencer Graves wrote:
You could think of 'lmer(..., family=binomial)' as doing a separate
glm fit for each subject, with some shrinkage provided by the assumed
distribution of the random effect parameters for each subject. Since
your data are
On Sat, 2006-06-17 at 09:46 -0700, Spencer Graves wrote:
'lmer' RETURNS AN ERROR WHEN SAS NLMIXED RETURNS AN ANSWER
Like you, I would expect lmer to return an answer when SAS
NLMIXED does, and I'm concerned that it returns an error message instead.
Your example is not
On Sun, 2006-06-18 at 13:58 +0200, Douglas Bates wrote:
If I understand correctly Rick it trying to fit a model with random
effects on a binary response when there are either 1 or 2 observations
per group. I think that is very optimistic because there is so little
information available per
I'm using FC4 and R 2.3.1 to fit a mixed effects logistic regression.
The response is 0/1 and both the response and the age are the same for
each pair of observations for each subject (some observations are not
paired). For example:
id response age
10 30
10 30
21 55
2
On Wed, 2006-05-24 at 09:22 -0700, Charles C. Berry wrote:
On Tue, 23 May 2006, Christopher Brown wrote:
How can I compute a power analysis on a multi-factor within-subjects
design?
If you are capable of installing source packages and if you know what a
general linear hypothesis test
When I run lrm from the Design package, I get a warning about
contrasts when I include an ordinal variable:
Warning message:
Variable ordfac is an ordered factor.
You should set
options(contrasts=c(contr.treatment,contr.treatment))
or Design will not work properly. in: Design(eval(m,
On Wed, 2006-05-17 at 09:48 +, Mark Difford wrote:
Dear R-users,
I am a newbie to this site and a relative new-comer to S/R, so please tread
lightly, for you tread...
There have been several posting relating to problems with augPred() from the
nlme library. Here is a fix for one of
The irr package seems to install correctly:
install.packages(irr)
trying URL 'http://cran.us.r-project.org/src/contrib/irr_0.61.tar.gz'
Content type 'application/x-tar' length 13848 bytes
opened URL
==
downloaded 13Kb
* Installing *source* package
On Tue, 2006-05-16 at 13:51 -0700, Phil Spector wrote:
Rick -
You didn't say what operating system you're using, but I suppose
that it's UNIX-based, because you're using the tar.gz files.
If this is the case, the problem can be resolved by setting the
environmental variable LANG to an
Has anyone else noticed that gstat no longer handles 1-D data?
library(gstat)
coordinates(pm.df) - ~x
Error in validObject(.Object) : invalid class SpatialPoints object:
spatial.dimension should be 2 or more
variogram(pm~1,~x,data=pm.df)
Error in validObject(.Object) : invalid class
On Mon, 2006-05-01 at 13:26 -0400, John Kane wrote:
This is a simple question but I cannot seem to find
the answer.
I have two vectors but with missing data and I want to
add them together with
the NA's being ignored.
Clearly I need to get the NA ignored. na.action?
I have done some
On Sun, 2006-04-16 at 19:10 +0100, Ramón Casero Cañas wrote:
Thanks for your suggestions, Michael. It took me some time to figure out
how to do this in R (as trivial as it may be for others). Some comments
about what I've done follow, in case anyone is interested.
The problem is a)
When I try to run the example from Variogram with an lme object, I get
an error (although summary works):
R : Copyright 2005, The R Foundation for Statistical Computing
Version 2.2.1 (2005-12-20 r36812)
ISBN 3-900051-07-0
...
fm1 - lme(weight ~ Time * Diet, BodyWeight, ~ Time | Rat)
Error:
I started my laptop, opened a shell and get this error message:
R : Copyright 2005, The R Foundation for Statistical Computing
Version 2.2.1 (2005-12-20 r36812)
ISBN 3-900051-07-0
lines deleted
Error in fun(...) : couldn't find function assignInNamespace
Error: .onLoad failed in
On Sun, 2005-12-25 at 23:01 -0300, Petra Wallem wrote:
Hello every body, I am trying to do a factorial anova analysis
following this model:
model-anova(lm(responsevariable~factorA*factorB))
model-anova(lm(luz$dosel~luz$estado*luz$Bosque))
Df Sum Sq Mean Sq F valuePr(F)
estado
On Thu, 2005-12-01 at 10:13 +, Prof Brian Ripley wrote:
On Thu, 1 Dec 2005, Martin Maechler wrote:
Rick == Rick Bilonick [EMAIL PROTECTED]
on Wed, 30 Nov 2005 23:11:07 -0500 writes:
Rick I'm trying to fit a generalized mixed effects model to a data set
where
Rick each
I'm trying to fit a generalized mixed effects model to a data set where
each subject has paired categorical responses y (so I'm trying to use a
binomial logit link). There are about 183 observations and one
explanatory factor x. I'm trying to fit something like:
(lmer(y~x+(1|subject)))
I also
On Mon, 2005-11-14 at 22:55 +, Walter R. Paczkowski wrote:
Hi,
I'm struggling with foreign to import a SAS file. The file, for lack of
imagination, is d.sas7bdat and is in my root directory (c:\) under Windows
XP. When I type
read.ssd(c:\\, d)
which I think I'm suppose to
Charles Dupont wrote:
Marc Schwartz (via MN) wrote:
On Tue, 2005-10-11 at 10:01 -0400, Rick Bilonick wrote:
I'm using R 2.2.0 on an up-to-date version of Fedora Core 4 with the
latest version of Hmisc. When I run an example from the latex
function I
get the following:
x - matrix(1:6
I'm using R 2.2.0 on an up-to-date version of Fedora Core 4 with the
latest version of Hmisc. When I run an example from the latex function I
get the following:
x - matrix(1:6, nrow=2, dimnames=list(c('a','b'),c('c','d','enLine
2')))
x
c d enLine 2
a 1 35
b 2 46
latex(x) #
Landini Massimiliano wrote:
On Tue, 25 Jan 2005 15:42:45 +0100, you wrote:
|=[:o) Dear R users,
|=[:o)
|=[:o) Is it reasonable to transform data (measurements of plant height) to the
|=[:o) power of 1/4? I´ve used boxcox(response~A*B) and lambda was close to 0.25.
|=[:o)
IMHO (I'm far to
Stephen Henderson wrote:
Hello
I'm moving from using R 1.8 for Windows to using Linux (Redhat version 9)
and I cannot get any graphics. However everything else maths, models
equations is fine-- and much quicker. I built from the source file following
the commands in the install manual.
I've
Suppose you estimate the ARIMA(p,d,q) paramters for an input x[t] using
the arima function. Is there an easy way to apply these values to the
output y[t] for transfer function modeling? For example, if I estimate a
(2,1,1) ARIMA for x[t] with ar(1) = 0.5882, ar(2) = -0.01517, and ma(1)
=
I'm still having problems installing rimage - the installation can't
find the fftw headers. As suggested, I installed the fftw rpm (for RH 9
from freshrpms). It installed without any errors or warnings. Yet I get
exactly the same error message - it can't find the fftw headers.
What do I have
The rimage install can't find the ffw header. Any idea why?
Rick B.
install.packages(rimage)
trying URL `http://cran.r-project.org/src/contrib/PACKAGES'
Content type `text/plain; charset=iso-8859-1' length 130159 bytes
opened URL
.. .. .. .. ..
..
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